Evolution’s Speed – How Common Are Single Insertions and Deletions?

I might have figured out how to push evolution to its limit in a lab, but I need to find if it would be practical. To do that, I need to know how common a good mutation must be if life really appeared by evolution. I’m starting by reading up on the different kinds of mutations. In my previous post I covered point substitution mutations, and in this post, I’ll cover insertions and deletions – also known as indels.

I soon found that I’d bitten off more than I could chew – at least in a single Sunday. Even though the human genome has been sequenced, gene sequencing technology is primitive enough that scientists have a lot of trouble finding even basic things like mutation rates. I found what looks like one of the first studies on mutation rates that gives a big-picture view. It was published two years ago, in June 2014. I didn’t expect that I’d have to look for answers in the bleeding edge of genetics research.

This study found that insertions/deletions/indels are far rarer than substitutions (~3 indels per 100 substitutions). The indel mutation rate was 5.03 ± 0.99 × 10−12 per letter (base pair) per generation. In other words, there are somewhere in the neighborhood of 5 insertions/deletions per trillion letters copied.

Due to Drake’s rule, it’s probably a good idea for me to calculate the per-genome indel mutation rate as well. The study didn’t mention this rate, and it also didn’t give the size of its genome, so I’ll have to calculate it myself. The genome of this species of yeast is somewhere in the ballpark of 11,600,000 genetic letters (base pairs), or 11.60 Mbp. Some estimates are slightly higher or lower. The lowest is 11.51 Mbp, and the highest is 12.10 Mbp. This means that the per-genome indel mutation rate is somewhere in the ballpark of (11.60 * 106) * (5.03 ± 0.99 × 10−12) = 58.348 ± 11.484 × 10-6 = 5.8348 ± 11.484 × 10-5. In other words, somewhere around 5 in 100,000 yeast cells will have an insertion or deletion mutation.

In case the link to my source for the size of this yeast’s genome breaks, here’s the site that I got it from. To find the data I got, search for genus saccharomyces and species cerevisiae.

This study is quite a find. I’ll probably use it as my main source for the rest of these mutation posts.

EDIT: interestingly, the study said that deletion mutations are more common than insertions. If this is true across the board, then it probably means there is genetic code that isn’t used all the time, and it sometimes disappears without any immediate effects. This is not what one would expect if life appeared by evolution. It’s also not what happens in my simulator. In my simulator, when a piece of code breaks, it tends to become random junk code that grows over time. However, I haven’t yet tried creatures that have code for a special case. I’ll have to look into that eventually.